Urban-industrial symbiosis (UIS) is an important system innovation via sectors integration, and has been widely recognized as a novel pathway for achieving regional eco-industrial development. Eco-efficiency, as a mature approach and indicator, offers an effective tool to uncover both the status and trends of such a transformation. However, most studies have focused on the whole industry or city as a whole, which has meant that a view from the sectoral level focusing on UIS was missing. To fill this research gap, this paper applied a modified eco-efficiency approach using integrating input-output analysis (IOA) and carbon footprint (CFP) to identify the eco-efficiency benefits of UIS from a sectoral level. Specifically, sector-level economic data (as economic outputs) and CFP (as environmental impacts) are used to calculate the sectoral eco-efficiency. IOA helps to offer sectoral economic data, and, with integrating process-based inventory analysis, to conduct a CFP calculation at the sectoral level. To test the feasibility of the developed approach, urban industrial symbiosis scenarios in one typical industrial city of China were analyzed. This city is held up as the national pilot of the circular economy, low-carbon city, and ecological civilization in China. Scenarios analysis on a business as usual (no UIS) and with UIS implementation in 2012 were undertaken and compared with the change of sectoral CFP and eco-efficiency. The results highlighted a moderate increase in eco-efficiency and trade-offs in certain sectors, indicating that UIS was moderately effective in increasing the urban resource efficiency from a sectoral level, but a refined design was required. Policy recommendations are made based on the analytical results, to inform decision makers and urban and industrial managers seeking to improve the implementation of UIS as a means of achieving greater urban sustainability.